Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants to BI Supervisor: Richard Hsung Professor, Dr. Wei Jing Student: Fu Jianjian Subject: Pharmaceutical chemistry

Click to add title in here Experimental plan Topic schedule implementation scheme References Outline 1 Introduction to research topics 2 2 Current research situation at home and abroad

1 Introduction to my research HCV is a serious and growing threat to human health –HCV NS3/4A serine protease is a trypsin-like protease essential for RNA replication. --- Drug resistance of HCV NS3/4A protease often occurs to its inhibitors. –BI201335, a competitive inhibitor contains a unique C-terminal carboxylic acid that binds noncovalently to the active site is in phase3 of clinical trials,which is devoleped by Boehringer Ingelheim incoportion –To data,there have not any report to the drug resistant mechanism research to BI201335

1 Introduction to my research Method Objective Contents Structural change responsible for the drug resistance Energetic changes responsible for drug resistance Research method and objective Description of the contents Using the molecular dynamics simulations, when the complex is stable, calculate the binding free energy analyse the xianghuzuo Yong between the protease and the inhibitor

1 Introduction to my research 2)May be critical for the development of novel inhibitors that are less susceptible to drug resistance. Significance of the topic 1)provide some insights into the resistance mechanism of NS3/4A protease mutants to BI201335

2 Current research situation at home and abroad The molecular dynamics is widely used to evaluate the drug resistance mechanism in HIV drugs and anti-cancer drugs. 1 Chunli Yan,Comparative molecular dynamics simulations of histone deacetylase- like protein:Binding hydroxamic acid inhibitors.Proteins.2009,73(1): GU HUI et al.Molecular dynamics simulations exploring drug resistance in HIV-1 protease.Bioinformatics.2010,55(24): Yufeng Cai et al.Differential Flap Dynamics in Wild-Type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation. J. Chem. Theory Comput., 2012, 8 (10): 3452–3462.

3 Experimental plan Research contents Step three Content analysis Step one Preparation of initial structures Step four Results and conclusions Step two Molecular dynamics simulations

Preparation of initial structures 1 Download the X-ray crystal structure of wild-type HCV NS3/4A protease complexed with BI MOE software will be applied to generate the 3D structure of the studies mutants (eghit complexes including the wild type one) in complex with BI by substituting specific residues using the wide type model as the template.

Do molecular dynamics using the Amber10.0 software package. The general Amber force field (GAFF) used to generated the small molecular parameters Prepare the inhibitors parameters with Antechamber module of Amber10 package.. The standard AMBER force field (ff99SB) will be used to decribe the protein parameters Do molecular dynamics using the Amber10.0 software package Molecular dynamics simulations

Content analysis Dynamics stability Root-mean square Deviation (RMSD) MM-PBSA approach Binding free energy Hbond and distance Ptraj script Decompose the total binding energy to each residue. Decompose energy

Results and conclusions Text in here The resistance mechanism

4 Topic schedule %96% 35% 70% Month 3-Month 6 Literature research Data reduction Month 12–Month 3 The first draft of a paper 2012 Month 11- Month 3l iterature review opening speech Month 8-Month 11th eoretical research Construct paper basic framework Month 4-Month 5 final manuscripts Print Finisher prepare for the spee ch 2011First half of 2012Latter half of

5 References [1] Diane Thibeault at el. Sensitivity of NS3 Serine Proteases from Hepatitis C Virus Genotypes 2 and 3 to the Inhibitor BILN JOURNAL OF VIROLOGY,2004,78(14) :7352–7359 [2] Christopher T. Lemke et al.Combined X-ray, NMR, and Kinetic Analyses Reveal Uncommon Binding Characteristics of the Hepatitis C Virus NS3-NS4A Protease Inhibitor BI The journal of biological CHEMISTRY,2011,286(13):11434 – [3] Paul Y. Kwo.Boceprevir: a novel nonstructural 3 (NS3) protease inhibitor for the treatment of chronic hepatitis C infection. Therapeutic Advances in Gastroenterology. (2012) 5(3) 179 –188. [4] Jean-Michel Pawlotsky.Therapeutic implications of hepatitis C virus resistance to antiviral drugs. Therapeutic Advances in Gastroenterology. (2009) 2(4) 205–219. [5] Paul Y. Kwo.Boceprevir: a novel nonstructural 3 (NS3) protease inhibitor for the treatment of chronic hepatitis C infection. Therapeutic Advances in Gastroenterology. (2012) 5(3) 179 –188. [6] Chunli Yan,Comparative molecular dynamics simulations of histone deacetylase- like protein:Binding hydroxamic acid inhibitors.Proteins.2009,73(1):

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